Workspace preparation

setwd("Documents/PROJECTS/Chap2")

library(marmap)
library(pander)
library(raster)
library(reshape2)
library(sf)
library(stats)
library(tidyverse)

source("C2_data_import.R")

Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.

2. Modelling of human activities influence (WIP)

The influence of each human activity has been modelled at each station, in order to be later used in HMSC models.

We calculated a probability of influence for each activity \(P_{ij}\). For non-fisheries activities, the index \(I_{ij}\) has been calculated based on the distance from the source(s), bathymetry and hydrodynamics influences. We also included a weighting parameter specific for each activity, .

\[ P_{ij} = w_{j} . I_{ij} \]

\[ I_{ij} = \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . f_{j} \left( 1 - \frac{D_{ij}}{D_{max, j}} \right) . \Delta Z_{i} . H_{i} \]

• \(i\) is a station
• \(j\) is a human activity
• \(f_{j}\) is the decay function of activity \(j\)
• \(w_{j}\) is the weighting parameter for activity \(j\)
• \(D_{ij}\) is the distance of station \(i\) from the source of activity \(j\)
• \(\Delta Z_{i}\) is the bathymetry index at station \(i\)
• \(H_{i}\) is the hydrodynamic index at station \(i\)